X-SOLVATE is a function within QUANTA X-BUILD or X-AUTOFIT which allows you to search an electron density map (fo-fc, 2fo-fc, or 3fo-fc) for water peaks, to adjust the peak positions, and to save them as water coordinates. If you have a license for X-BUILD or X-AUTOFIT, X-SOLVATE is automatically available from the QUANTA Applications menu.
This chapter describes the functions and steps that you take to use X-SOLVATE. It covers the following areas:
X-SOLVATE requires at least one MSF file and allows you to supply other MSF files containing coordinate data. When doing non-bonding calculations, X-SOLVATE will use the coordinates from all MSF files that were open at X-SOLVATE's start-up. New water positions will only be determined if there are no atomic coordinates from any of the MSF files within the minimum cutoff distance from an electron density peak. This means that waters that X-SOLVATE previously placed will be used in the non-bonding calculations and new waters will not be placed at these previously determined sites.
When you exit X-SOLVATE, the waters will be saved in one of several places, depending on the currently open MSF files.
1. If any MSF currently open and active has any water molecules (including those placed previously by X-SOLVATE), then the new water molecule will be inserted in this MSF after the last water already here. The sequence ID of the new water molecules appended to this dataset will be started at the last sequence ID + 1 to give consecutive numbering of all the waters. The segment ID will be the same as the segment ID of the current waters in this MSF.
2. If none of the currently open and active MSF files have any water molecules, then a new MSF file, called searchwaters.msf, will be added to the molecular table and all the new water positions will be added to this file. The first sequence ID will be 1 and the new segment name will be W.
Load the coordinate set of a molecule into QUANTA. Also supply an electron density map (fo-fc, 2fo-fc, or 3fo-fc) and the current symmetry for the crystal system of the original data.
You can use the routine without symmetry but, if you do, no peak checking is carried out for symmetry equivalents. This produces water molecules related by symmetry overlapping.
Note that symmetry atoms can be picked and the information displayed.
1. Select X-Solvate from the Applications menu. QUANTA saves the current selection, color, and display masks. It then generates a selection mask that contains all atoms plus their symmetry equivalents for the map currently loaded.
The color mask is set so that the working molecule is colored by element, and the symmetry-equivalent atom positions are colored blue and the NCS atoms red.
A three-dial set is displayed containing dials for xyz positioning of current water molecules. Additionally, the Search for peaks palette appears.
This section describes the steps for searching, adjusting, and saving water molecules.
A search for water molecules identifies the water peaks in the electron density map and sorts them by size. X-SOLVATE is designed to run searches in shells. The first search finds water around the protein as defined by the max-bond parameter. If all water molecules from this search are saved, a subsequent search finds the next level of water molecules further from the protein.
1. Select Search for waters from the Search for peaks palette. A search is initiated for peaks that:
Peaks are returned in size-sorted order, where the first peak is the largest in the map. The molecule window changes so that the view is centered on the first peak and a 6.0-Å sphere of the map displayed. Atom contacts to the peak are shown by white dotted lines and numbers indicating distances (up to 3.5Å). The program maintains non-bond information of 6.0 Å for each water, so if you move the water more than 2.5 Å, the nonbond data will be incorrect.
2. Select Next peak from the Search for peaks palette to move to the next peak. The Molecule window display adjusts accordingly.
3. Select Previous peak from the Search for peaks palette to return to the peak you have just finished examining.
You can adjust the parameters for a search by selecting Change search setting... in the Search for peaks palette. A dialog box is displayed.
For an explanation of each of the parameters, see Peak search parameters dialog box.
After examining the water molecules identified by the search, you can manipulate each of them individually to position them as you want.
1. Zoom in on the water so that you can see its position relative to the atoms around it.
2. Adjust the position of the water using the dial set that is displayed.
The non-bonds and hydrogen bonds to each water appear as white and yellow lines (color 5 and 6). The white lines represent hydrogen bonds to atoms and the yellow lines are non-bond interactions. The non-bonding and hydrogen bonds up to 3.5Å are shown.
On completion of checking the water site for nonbonds and fit to density, this water position can be saved. The tool Save as water on the Search for peaks palette will place a water molecule at the peak site. If this water molecule on subsequent analysis is required to be deleted, then the Delete water tool will remove the water molecule associated with this peak in the electron density.
X-SOLVATE saves the water in its current position in a currently open and active MSF file only if this file already contains water molecules. If not, then a new file searchwaters.msf is created.
You can save all water peaks that are identified in a search by selecting Save all peaks from the Search for peaks palette.
This section provides quick-reference to information on the Search for peaks palette selection. This palette provides tools for searching for water peaks, examining the peaks, and saving them.
Access the Search for peaks palette by selecting X-Solvate from the Applications menu in the QUANTA menu bar.
Use his selection to initiate a search of the current molecule for the peaks that:
Use this selection to change the parameters used in the calculation. For information on parameter settings, see Peak search parameters dialog box.
Use this selection to move the search center in the display. Place the new center of the calculations using the 3D cursor that is provided. The default center is the geometric center of the molecule.
Use this selection to toggle the current map display on and off.
Use this selection to move the display so that it is centered on the previous peak from the peaks list. This peak can then be manipulated and saved as a water molecule.
Use this selection to move the display so that it is centered on the next peak in the peaks list. This peak can then be manipulated and saved as a water molecule.
Use this selection to move the display so that it is centered on a specific peak in the peaks list.
This peak can then be manipulated and saved as a water molecule.
Use this selection to mark a peak to be saved on exit from X-SOLVATE to the .msf file at the current water position.
Use this selection to mark a peak not to be saved on exit from X-SOLVATE to the .msf file at the current water position.
Use this selection to mark all waters so that they are saved on exit from X-SOLVATE.
Use this selection to exit from X-SOLVATE and to save the water molecules in the .msf file.
Use this selection to exit from X-SOLVATE when you do not want to save the peaks. Previous selection, color, and display masks are restored.
This section provides quick-reference information on the Peak search parameters dialog box options. This dialog box provides parameter options peak searches.
Access the Peak search parameters dialog box by selecting Change search setting... on the Search for peaks palette. This dialog box allows you to change the parameters that are set for a water search.
This is the minimum value of electron density in sigma where a water can be placed. The default value is 2.
This is the minimum distance possible for a peak to be from the protein. The default value is 2.0 Å. This resolution is less than the reasonable minimum expected in high resolution maps so that error inherent in the maps at this stage does not prevent determination of the water positions.
This is the maximum distance from the protein that a water peak is found. The default value is 5.0 Å. The setting prevents X-SOLVATE from finding peaks in a density region where no other data justifies placing one. The aim of the routine is to find the first solvation shell, then to repeat the peak search with the first solvent shell present, thus allowing the determination of further solvent shells by iteration.
This is the minimum distance allowed between peaks. Peaks that are closer together than the min-sep value are replaced by a single peak in the average position. The default value is 1 Å. The value used here depends on your working practice; either multiple waters are placed close to each other with low occupancy, or single unit occupancy sites can be placed with minimum separation of 2.5 Å.
This is the radius that describes the region to be searched by X-SOLVATE. The default value is calculated from the current loaded macromolecule so as to cover the entire molecule.
This changes the map display radius about each peak. The default value is 6.0 Å.
This is the BVALUE of the temperature factor saved with the water position coordinates. The default value is 20.